data_6VEC # _model_server_result.job_id vNihHd1wK1mLwiBrBuXLOg _model_server_result.datetime_utc '2024-11-29 07:57:21' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6vec # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":401}' # _entry.id 6VEC # _exptl.entry_id 6VEC _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 11 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6VEC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VEC _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 22-meric _pdbx_struct_assembly.oligomeric_count 22 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 W N N ? 3 Y N N ? 3 AA N N ? 3 CA N N ? 3 EA N N ? 3 GA N N ? 3 IA N N ? 3 KA N N ? 3 MA N N ? 3 OA N N ? 3 QA N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 W O1B ADP . A ADP 401 1_555 X MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc2 Y O1B ADP . B ADP 401 1_555 Z MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc3 AA O1B ADP . C ADP 401 1_555 BA MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc4 CA O1B ADP . D ADP 401 1_555 DA MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc5 EA O1B ADP . E ADP 401 1_555 FA MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc6 GA O1B ADP . F ADP 401 1_555 HA MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc7 IA O1B ADP . G ADP 401 1_555 JA MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc8 KA O1B ADP . H ADP 401 1_555 LA MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc9 MA O1B ADP . I ADP 401 1_555 NA MG MG . I MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc10 OA O1B ADP . J ADP 401 1_555 PA MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc11 QA O1B ADP . K ADP 401 1_555 RA MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6VEC _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code W 3 ADP A 1 401 401 ADP ADP . X 4 MG A 1 402 402 MG MG . Y 3 ADP B 1 401 401 ADP ADP . Z 4 MG B 1 402 402 MG MG . AA 3 ADP C 1 401 401 ADP ADP . BA 4 MG C 1 402 402 MG MG . CA 3 ADP D 1 401 401 ADP ADP . DA 4 MG D 1 402 402 MG MG . EA 3 ADP E 1 401 401 ADP ADP . FA 4 MG E 1 402 402 MG MG . GA 3 ADP F 1 401 401 ADP ADP . HA 4 MG F 1 402 402 MG MG . IA 3 ADP G 1 401 401 ADP ADP . JA 4 MG G 1 402 402 MG MG . KA 3 ADP H 1 401 401 ADP ADP . LA 4 MG H 1 402 402 MG MG . MA 3 ADP I 1 401 401 ADP ADP . NA 4 MG I 1 402 402 MG MG . OA 3 ADP J 1 401 401 ADP ADP . PA 4 MG J 1 402 402 MG MG . QA 3 ADP K 1 401 401 ADP ADP . RA 4 MG K 1 402 402 MG MG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . AA 3 187.76 194.56 137.056 1 48.07 ? PB ADP 401 C 1 HETATM 2 O O1B ADP . . . AA 3 188.201 194.586 135.616 1 48.07 ? O1B ADP 401 C 1 HETATM 3 O O2B ADP . . . AA 3 188.012 195.849 137.795 1 48.07 ? O2B ADP 401 C 1 HETATM 4 O O3B ADP . . . AA 3 186.407 193.938 137.29 1 48.07 ? O3B ADP 401 C 1 HETATM 5 P PA ADP . . . AA 3 190.34 193.948 137.778 1 48.07 ? PA ADP 401 C 1 HETATM 6 O O1A ADP . . . AA 3 190.786 194.076 136.344 1 48.07 ? O1A ADP 401 C 1 HETATM 7 O O2A ADP . . . AA 3 190.486 195.117 138.718 1 48.07 ? O2A ADP 401 C 1 HETATM 8 O O3A ADP . . . AA 3 188.789 193.546 137.753 1 48.07 ? O3A ADP 401 C 1 HETATM 9 O O5' ADP . . . AA 3 191.037 192.661 138.44 1 48.07 ? O5' ADP 401 C 1 HETATM 10 C C5' ADP . . . AA 3 191.173 192.64 139.854 1 48.07 ? C5' ADP 401 C 1 HETATM 11 C C4' ADP . . . AA 3 191.17 191.213 140.397 1 48.07 ? C4' ADP 401 C 1 HETATM 12 O O4' ADP . . . AA 3 192.448 190.6 140.302 1 48.07 ? O4' ADP 401 C 1 HETATM 13 C C3' ADP . . . AA 3 190.774 191.175 141.861 1 48.07 ? C3' ADP 401 C 1 HETATM 14 O O3' ADP . . . AA 3 189.452 190.642 141.959 1 48.07 ? O3' ADP 401 C 1 HETATM 15 C C2' ADP . . . AA 3 191.787 190.299 142.563 1 48.07 ? C2' ADP 401 C 1 HETATM 16 O O2' ADP . . . AA 3 191.137 189.177 143.157 1 48.07 ? O2' ADP 401 C 1 HETATM 17 C C1' ADP . . . AA 3 192.749 189.851 141.475 1 48.07 ? C1' ADP 401 C 1 HETATM 18 N N9 ADP . . . AA 3 194.186 190.075 141.762 1 48.07 ? N9 ADP 401 C 1 HETATM 19 C C8 ADP . . . AA 3 194.773 191.222 142.152 1 48.07 ? C8 ADP 401 C 1 HETATM 20 N N7 ADP . . . AA 3 196.11 191.054 142.298 1 48.07 ? N7 ADP 401 C 1 HETATM 21 C C5 ADP . . . AA 3 196.391 189.782 141.978 1 48.07 ? C5 ADP 401 C 1 HETATM 22 C C6 ADP . . . AA 3 197.602 188.944 141.916 1 48.07 ? C6 ADP 401 C 1 HETATM 23 N N6 ADP . . . AA 3 198.811 189.456 142.231 1 48.07 ? N6 ADP 401 C 1 HETATM 24 N N1 ADP . . . AA 3 197.458 187.66 141.535 1 48.07 ? N1 ADP 401 C 1 HETATM 25 C C2 ADP . . . AA 3 196.26 187.142 141.221 1 48.07 ? C2 ADP 401 C 1 HETATM 26 N N3 ADP . . . AA 3 195.122 187.849 141.258 1 48.07 ? N3 ADP 401 C 1 HETATM 27 C C4 ADP . . . AA 3 195.123 189.146 141.625 1 48.07 ? C4 ADP 401 C 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 72 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #